Evangelion Ultimate: The Phantom
by xennophobia
Summary: Shinji Ikari was lovingly raised to make a difference. However even as a pilot, Shinji found he could do very little. Taking to the night, he vowed to save the world as a masked vigilante. Will Shinji be able to hide his secret from NERV, Misato, Asuka and his classmates? Shinji x Asuka goodness in later chapters.
1. Prologue Pt 01

**Evangelion Ultimate**

**Prologue Pt. 01**

**Hello all. This is something I've put some thought into for awhile and I really wanted to give it a shot. It's nothing special, just a continuation of Evangelion with a bit more fluff, some more plot, and the possibility for our our beloved characters to discover a bit more about themselves. That being said, just enjoy!**

**Shinji x Asuka is our pairing here, don't worry, it'll be here soon enough!**

* * *

Shinji Ikari and Mari Makinami Illustrious ran as fast as their eight year old bodies would allow, their pockets stuffed full of their spoils from a day of petty theft and pickpocketing. Both laughed gingerly the pair stopping in a nearby alley, quietly giggling. Dumping their pockets, a pile of money, snack food and various curios poured onto the ground in a magnificent pile. While the snacks were great, and a little souvenir looked good every now and then, the real prize was the wads of money the had come back with. Mari gingerly started counting what they had, while Shinji pulled the rest into a plastic shopping bag.

"We did great!" She declared, smiling at Shinji, "You're actually really good at this!"

Shinji smiled back, "I just hope they don't realize anytime soon."

"YOU LITTLE SHITS! GET BACK HERE!" A voice rang out in the distance. Mari and Shinji immediately bolted from their alleyway, flying through the small desolate town at a breakneck pace. Shinji didn't turn to look, he just kept running, fairly certain someone had just tried to clobber him with a rock. Mari sprinted just behind him, " Slow down...I can't...keep up!" She huffed. Fear was one of Shinji's biggest motivators, and right now he was afraid of what his mama would do if she found out. With that in mind, he bolted even faster through the cool evening air. The sun was quickly setting on the mountainside village, and the pair was counting on the darkness of night to come soon and let them whisk away undetected. Shinji had turned from the path and darted into trees, Mari barely catching up as the shadowy figures of their pursuers followed in the distance.

"God dammit!", Young Shinji cursed, "Why did I have to open my mouth..."

They found cover in thick foliage, carefully watching their pursuers in the distance as the group searched for the two kids, while the steady approach of night turned the world into a comforting twilight. Soon the group gave up and began to disperse, and the pair assumed they were alone.

"Shinji..." Mari panted, "...How the hell do you run so fast?"

Shinji shrugged, mildly winded. Even without fear, running had never really been a chore for him, and he guessed his own endurance was mostly natural. He grimaced, realizing that in the process of diving into the brush, he had scratched and scuffed himself up, and his clothing was littered with grass and mud stains. Mari hadn't fared any better. Her red glasses sat crooked on her nose while her hair was full of leaves and dirt. Her attire was pretty much destroyed as she had dove in and ripped her shirt on a branch. He could see the distinct sign of a poison ivy rash beginning on her arms, but said anything. Mari wouldn't let him tend to it either way. The two caught their breath and begin to leave, but soon realized they were not alone.

"Well, well..." A man's voice rumbled, " So you two are the one's that have been robbing this town blind."

"K-Kaji..." Shinji barely got out, "Please don't tell anyone!"

"Y-yea, please!", Mari dove on her knees and begin to grovel.

Kaji looked the two over with a smile. The dark haired man had a cigarette between his lips, and was dressed casually. They had known him loosely for awhile now as he was a frequenter of the local bar, and they had seen him sitting out many times with friends or shopping at the local grocery store. They had held conversations with him, and for awhile had been the bane of his existence with their nonstop stalking of him, both agreeing that he was interesting for an adult.

"What are you doing out here?" Shinji asked, realizing that his presence was even stranger than there own.

"A little star gazing." He replied, gesturing to the telescope set up on a tripod beside him, however the telescope was not pointed at the sky, however pointed downwards from the tree covered hill they now stood pointing at the military installation sitting at the base of the mountain. Shinji and Mari both noticed this, and were both beginning to feel wary of Kaji. "Why don't you two help me pack up and I'll give you a ride home?", he asked.

Mari and Shinji could tell by the tone of his voice that this wasn't a suggestion, it was more of an order. He was a kind man, but they could tell he wasn't going to let them just walk away. Reluctantly the two assisted him and soon the three were walking down the hill, carrying various bags. Kaji's car was parked on the side of the road nearby, and the three soon entered and were on there way. It was mostly a silent trip as both children weren't entirely sure that whether or not he was going to divulge to their guardian the details of their evening.

Soon they pulled up in front of a derelict Japanese temple, their mother standing at the gates, her arms crossed. Shinji was sure he and Mari were in trouble. The two children reluctantly exited along with Kaji, the three walking up to the gate slowly, the two children slowing their gate intentionally, hoping to prolong the inevitable.

"Nancy." Kaji greeted, giving her a smile, "I found these two in the middle of nowhere."

"I wonder what they were doing there." The blonde haired woman frowned, "Hiding no doubt."

"M-Mama..." Shinji started, but was quickly cut off by the blue eyed woman.

"And what do we have here?" Nancy walked up to Shinji plucking the bag out of his hands and inspecting the contents.

"Junk food?" She smirked, "Nothing but sweets and fat filled treats. I'll take these."

Shinji didn't protest, letting her confiscate their stolen goods. He gulped knowing that his mama's punishment would be swift and devastating. The blonde stepped over to little Mari and swiftly reached in her pockets, pulling a rather generous wad of money out, " I think I'll keep this too."

"W-What?!" Mari cried trying to grab it back out of the woman's hand, " Give it back!"

Shinji could have sworn he heard Kaji chuckle lightly behind them.

"Both of you should clean up and get to bed. We're getting up bright and early tomorrow." Shinji and Mari both gulped. They knew what was coming, and there wasn't anyone in heaven or hell that could intervene. Slowly both children walked past her into their home. Kaji and Nancy were left, both giving a smile to each other.

"How's he doing?" Kaji asked quietly.

"Who? Shinji?" Nancy replied, "Well enough. Mari being around has helped him loads, even if it isn't in the most morally 'correct' ways."

"How have you gotten around his father?" Kaji produced a cigarette, soon lighting it, then passing one to Nancy.

"We've been creative." Nancy replied between puffs, " It's just a matter of getting that old man to report to his bastard of a father every now and then. No chance in hell his father's precious little 'scenario' is going to happen again."

"And what does Shinji know?" The dark haired man glanced towards the sky as the smoke disappeared into the darkness.

"He knows enough. I don't think he wants to be a messiah, I just think he wants to be happy, and that's exactly what we need.", Nancy puffed briskly, also giving the dark star filled sky above them a quick glance.

"You believe that striving for his own happiness will save us all?"

"He's kind hearted. He cares about others. When he has the tools and abilities along with the drive, he'll see this through to the end and stop this endless, pointless war."

"Does Mari have anything to do with that drive?" Kaji jokingly asked, referring to the obvious little stunt the two had pulled.

"A bit, but I they're definitely not going to get married or anything. His little heart is tied to another."

"And who would that be?" Kaji glanced back to her giving a smile. He was indeed curious.

"A fiery little German redhead. Trust me, you'll know her when you see her." Nancy nearly laughed, "She's a real firecracker, not the kind you'd expect our little Shinji to go for, but trust me, they're meant for each other."

"Destiny is a strange, strange thing." Kaji whisped as he finished his cigarette, turning to leave.

Shinji was woken by the loud crack of his door being slid open. Nancy stood before him and he dashed to get dressed. Morning had finally come, and with the crack of the sun, also came the crack of the proverbial whip that she was about to beat him with. He soon exited his room, the blonde haired, blue eyed woman walking briskly behind him as they stepped out into the courtyard where Mari was already waiting. The two knew what was coming. In addition to their normal school routine, to which Nancy served as their instructor, they would also have an insane amount of physical drilling ahead of them, on top of their normal lessons in martial arts.

Silence descended as the two awaited for their guardian to start talking. The morning air was cool, the sun barely peeking over the horizon as bugs danced across the garden in the courtyard, various botanical in bright and vivid summer bloom all centered around several small ponds. It was part of Mari and Shinji's chores to tend to the garden and courtyard, and they had quickly become well versed in gardening and landscaping, all under the careful instruction of their blonde guardian. The woman was a bit rough around the edges, but genuinely kind. She pushed them in ways both found a bit odd, but neither thought of it too much. In many ways the structure that she had given them was in stark contrast to the states of their previous lives, and both had accepted it happily. But now both wished that they could be anywhere else but here. Nancy's retribution was swift and just, and both were well aware of the hell this woman could bring down on them.

"I'm not angry, I'm disappointed." Nancy started, "You robbed everyone blind, and you nearly got away with it."

"We'll never do it again!" Shinji and Mari cried in unison.

"No." Nancy said flatly, "You're going to learn to be better."

Both children looked absolutely flabbergasted. The pair looked at each other and back to their guardian, neither sure if they had heard her correctly.

"Yup, you heard right." She smiled back, " Now we're going to work on the most important part of performing a successful heist, cardio! Now run!"

Shinji and Mari couldn't in their lives recall running as much as they had. It had been at least four hours, from the crack of dawn to almost the afternoon. Nancy had called the two back finally as they had done lap after lap around the large estate, the cool morning air quickly heating up and becoming the searing summer heat the two were all too familiar with. Shinji and Mari had set to preparing lunch as Nancy set out their lessons for the day. While resting the two would be tutored, work on their daily schoolwork, and finally rise again to begin physical training. Today proved to be merciless, for as soon as they had completed all of their school work, Nancy ordered the pair to follow, she herself now wearing a casual outfit perfect for a daily workout. Shinji's head had began to spin as he was sure he had been thrown more times than he wanted to count. Mari, on the other hand, began to protest, unable to lift her arms anymore.

"Please stop!" Mari began, " My arms feel like noodles!"

Nancy turned to her, falling out of her offensive stance, Shinji once more on the ground behind her, " I suppose that is enough for today..." She smiled once more, "But don't think you're done quite yet, expect the same thing tomorrow."

"Please, no!" Shinji cried as he picked himself up.

Neither of the two enjoyed combat practice, but that seemed to be what most of their day was made of. As night came once more the air began to cool again, and both children were more than happy to sit on the porch and have dinner. Nancy patted the two on the head as they wolfed down their rice and vegetables, giving them a reassuring look as they glanced up on her. They both smiled back, knowing that someone cared about them.

Nancy soon took a seat beside them, the three conversing happily as they sat. At first, when she had received Shinji, this had been nothing but another assignment for this woman. She had left her own family, something that she was fully prepared to do, and expected to play babysitter for almost ten years, but as she found herself reading her briefing packet, she couldn't help but feel pity for the child. Almost immediately she had bonded with Shinji, and found herself absolutely in love with the four year old. She frowned at herself for letting him slip under her business facade so easily, but after a few months, she embraced it. Mari had come as a surprise, the orphan of a family killed just after second impact, her only remaining relative an older sister and co-worker of Nancy, who needed to leave on an extended assignment as well. Nancy had pulled some strings, and convinced her superiors of the positive effects a playmate would have on her charge, Shinji. At the age of five, Mari had moved in with them, and the woman was truly happy how the three of them had bonded.

'Mama' was a word that she was shocked to hear from Shinji's mouth when he was six. She had panicked at first, unsure of how to react. He had lost his mother only two years ago, and she hid in the bathroom, tears escaping her eyes. She had sat and thought for awhile, unsure of how to proceed. It wasn't supposed to be like this, she had her own family that she had to leave, and here she was with virtually another of her own. She had cried and sobbed, wanting so badly to accept it, but knowing that she was betraying her own family, forced to forsake her own children. Clarity had come when Mari had knocked on the door, asking if 'mama' was alright.

It was not their fault, neither of them asked for this, nor did she. It was the situation they were all stuck in, and they had to make the best of it. Collecting herself, she had rushed out, embracing the two children, scooping them up into her arms, tightly hugging the two as though they were her own children. They were indeed hers, she was increasingly becoming more sure of this.

_"Love is going to save us all."_

* * *

Yuuko Yagami sighed as she patted her dark hair down once more. The smell of burning hair lingered in the room, and she cursed silently, certain that she was going to have to chop off her hair a little below her shoulders in order not to look like a freak. She was in charge of the second child chosen by NERV, Asuka Langley Soryu, and the young girl was more excitable than any other child she had ever encountered.

"Where did you go, you little shit?" She cursed at the child who had hidden somewhere in the apartment the two occupied.

"Ooooh Asuka!", She mocked as she searched for the little red devil. Cunning was the best description of her charge, the eight year old redhead more than a handful. Entering their small kitchen, she carefully surveyed the area, knowing the child had probably hidden under the sink. She swiftly reached for the handle, pulling the small cupboard open, revealing the young girl. She tried to grab for her, but Asuka, with all her determination, dove at the woman, slipping through her arms and slipping away, running out of the kitchen and down the hall.

"GET BACK HERE!" Yuuko cried, lifting herself off the ground and giving chase.

"Kiss my ass!" Asuka cried as she slammed the door to her room. The sound of furniture being moved could be heard, no doubt the girl planned to barricade herself in. Yuuko sprinted through the hall, slamming into the door. On the other side Asuka had used a chair propped against the handle to buy time while she pushed her dresser up to the door.

"Fuck it!" Yuuko cried, the Japanese woman rearing her arm back and striking clean through the door. Asuka jumped as a hand exploded through the flimsy door, pushed the chair aside and turned the handle.

"Holy shit!" Asuka screamed, quickly diving for cover on the other side of her bed.

"Gotcha!", Yuuko dove towards her, catching Asuka by the neck of her shirt. Asuka didn't fight this time, still in shock that her guardian had just destroyed a door with a single stroke. Yuuko wasn't sure what to do as the expression on the little girl's face changed from shock to amusement.

"That was awesome!" The redhead exploded in excitement, her blue crystal eyes lighting up, "How did you do that?"

"Oh well...umm...I just punched it as hard as I could.", Yuuko rolled her eyes.

"Does it hurt?" Asuka asked, a tinge of worry evident in her voice.

"Oh like you wouldn't believe." Yuuko said with a hint of sarcasm. Both of them had lost their anger, and she let go of Asuka's collar, and sat on the child's bed, looking at the redhead with an exasperated expression.

"I-I really didn't mean to." Asuka started, looking at the ground, "I'm sorry."

"Why were you playing with fire in the first place, Asuka?" Yuuko replied, deep concern in her voice, " Where did you get the idea?"

"Some of the boys were talking about it. They said that you could make a flamethrower with a can of deodorant and a lighter!" Asuka cried back. It was clear she was just trying it out of curiosity. Yuuko let out a deep sigh. She took Asuka into her arms, holding the girl as strongly as she could.

"Asuka, that was dangerous. You could have set the apartment on fire, or worse, blown off your hand." She said, pulling the redhead out of her arms, looking her dead in the face as she held the girl in front of her. Asuka's bright blue eyes were too beautiful for words. Yuuko had been blown away by how cute the girl she'd been given was. It was evident that in less than four or five years she would have much more to worry about than just mothers pouring over her cuteness. Yuuko had let Asuka's auburn hair grow out, reaching almost past her waist. She kept it back in two red ribbons, her wild bangs hanging just above her eyes in a stylish but disheveled mess, contrasted with her alabaster skin, the girls cute appearance hid an explosive personality underneath that sometimes had to be kept in check. Yuuko sighed.

"Can you punch through the wall?" Asuka asked, her excitement mounting once more. She looked up at her caretaker expectantly. Yuuko could only sigh. The dark haired woman didn't even look towards the wall nearest the bed, her fist striking through the wall with ease, the drywall giving way easily.

"YAY!" Asuka cried, throwing her arms in the air, "Can I try?!"

"Why the hell not?" Yuuko replied, "The walls her are paper thin, and we're going to have to call maintenance to fix the door anyways..."

At this Asuka went up to the wall nearest the bed and reared her arm back. Unfortunately she chose wall nearest to the headboard of the bed, completely missing the wall and striking the infinitely more solid headboard.

"AAAAAAHHHH!" Asuka cried as her fist bounced off the headboard. She grabbed her hand, beginning to writhe in pain, tears forming as she clenched her eyes shut.

"GOD DAMMIT ASUKA!" Yuuko cried as she once again scooped up the girl in her arms.

Several hours later, along with a trip to the Hospital, the pair entered the apartment, fast food in hand, Yuuko giving an exasperated sigh. Asuka was a handful, but then again so was Yuuko herself. She remembered more than one time she had pissed her own mother off and the woman had chased them through their summer home, determined to catch and destroy her own child. Honestly Asuka had a good heart, and while she was a bit self absorbed, she could be kind and considerate.

"What did we learn today?" Yuuko asked as the two plopped on the couch.

"Don't do stupid shit." Asuka replied flatly. Her right arm was now bound to a bright red brace, the doctor caring for her having found the redhead to have cracked her wrist only slightly. Asuka had cried for a bit, but was mostly alright once they had arrived at the hospital. It had been a rather typical ordeal between the two, as Asuka seemed to have a penchant for trouble. Deeming that the pain the young girl had experienced was more than enough punishment, she had taken the young girl to her favorite fast food restaurant, hoping a cheeseburger and a shake would make up for Yuuko's own sub-par parenting. Yuuko considered herself in no way qualified to take care of a child, but she doubted any normal or sane person could handle Asuka. She had on multiple occasions had to stop the redhead from attempting to drive their car, and she had been called to Asuka's school on more than one occasion when Asuka had beaten up kids almost two years older than herself. On one occasion Asuka had actually managed to tie one of her classmates up in the women's restroom and was intent on torturing her victim. It didn't help that Yuuko's orders were to keep this child in top physical shape as well as supplement her school education with a ridiculous amount martial arts and defensive training. It was a wonder that Asuka hadn't killed anyone yet.

"So have you ever killed anyone?" Yuuko asked, glancing to the girl sitting next to her.

"Not yet." Asuka replied, "But I came close a few times." Yuuko could only smirked at the casual response the Asuka replied with.

"Any boys ask you out yet?"

"Boys are gross." Asuka spat, "They're good for nothing liars, Mama."

"You're going to be saying the exact opposite once you're a teenager." Yuuko smiled back.

"Never." The redhead replied, "I'm going to beat all of them until they're black and blue. There's a reason the only two Eva pilots are girls, because we're the best."

"Oh? Is that so?" Yuuko chucked, "I can tell you a little secret. The third pilot is a boy."

At this Asuka's eyes snapped to her guardian, "What? They chose a boy?" Asuka was entirely blown away.

"It's a secret, so don't tell anyone, but I know who it is."

"Really?" Asuka leaned close, forgetting about her meal, "Where is he? What does he look like?"

"He lives in Japan. And he's really nice, and cute, and I bet he'll really like you." Yuuko flicked Asuka's nose playfully, having the girl's attention entirely, " He plays the guitar and the cello, and he's a bit of a little shit, just like you. In fact, I think you may have met him already when you were younger."

"I have?" Young Asuka thought for a moment, "When?"

"Do you remember Miss Ikari?" The lady your mom worked with on Eva?" Yuuko replied, glancing up to the ceiling as she was thinking, "Her kid, Shinji?"

"Oh yea!" Asuka's eyes snapped back to Yuuko, " He was so mean! He took away my toys away when we used to play. But he liked me, just a little bit."

Yuuko gave a smile as the eight year old beside her started again on her burger. She seemed to be caught up in thought, no doubt thrilled that there was another pilot. She hadn't seemed that interested when Yuuko had told her about the first child, Rei Ayanami, but this was different, she seemed enthralled even more that it was someone that she knew. Yukko absolutely loved it when she could delight the child, as it would always divert Asuka's devious and a headstrong personality, and her true innocence would pour through.

"Mama? Can I sleep with you tonight?" Asuka asked, breaking Yuuko's thought process, " You kinda destroyed my room..."

"Of course." Yuuko nearly giggled.

**To Be Continued...**

* * *

**Well, let me know what you think! I always appreciate input! More will follow soon, I promise. The Prologue parts are going to be short, but the actual chapters are looking a bit beefier. I'm writing this in pieces and stringing them together because they're are so many events and characters going around! **


	2. Prologue Pt 02

**Evangelion Ultimate**

**Prologue Pt. 02**

**Hello Again! Whew, more backstory. I had to have rewritten this chapter at least four or five times. It has a bit of a more serious tone than the last, and as a prologue piece it still is setting up our romance to come. Just one more prologue chapter after this one, and we'll reach the main attraction, I promise!**

**Also, I've been working on correcting spelling and grammatical errors. I have a prereader on the way, and soon I should have those pesky mistakes completely out of this story. As for Misato and the Pilot's overall adjustment to the world around them, I'm really working on establishing what the interaction between Shinji and Misato will be like. I'm trying not to move Shinji and Asuka too far away from their original characters, but I'm hoping that just a tad bit of a push will help Asuka open up, and help Shinji push Shinji out of his shell ever so slightly. It's really turning out to be a balancing act.**

**Sorry, not much related to Asuka this time. This and the next piece will lead up to Shinji's debut as the pilot of Eva Unit 01, and help establish our world!**

**Enjoy!**

* * *

Nine year old Shinji lay on his bed while in his hands he held several pieces of paper. He looked intently at his own drawings.

"Watcha got there?" Mari appeared in the doorway, giving a light smile.

"N-nothing." Shinji replied, quickly folding the stack of papers and throwing them between his bed and the adjacent wall.

"You were drawing superheroes and robots again weren't you?" Mari laughed, diving across Shinji and digging in the crevice between the bed and the wall, Shinji desperately trying to push her away. Mari soon produced the folded papers and took off, running down the hall as Shiniji followed in close pursuit. Nancy glanced up from her magazine as she relaxed in the living room of their home. Mari and Shinji sprinted by, their guardian fairly indifferent to their fighting as long as they didn't destroy each other or any belongings of hers.

"I knew it! I knew it!" Mari cried as she had managed to unfold the paper and get good look just before Shinji tackled her. The two went rolling on the floor into the kitchen as Shinji tried to pull the papers from her hands.

"Why do you always have to do this?" He cried, as she slowly relinquished his drawings. He carefully went through the small stack making sure they were all there. It wasn't that he didn't want Mari to see his drawings, it was the fact that he was secretly drawing himself as a superhero. Mari merely knew that it was something Shinji got defensive about every time she approached him, so she made a game out of it whenever possible. She liked his attention and sometimes wished he'd be a bit more talkative to her, almost getting angry when she would be ignored.

She didn't get up from where she lay, only looking at the ceiling above lost in thought. Shinji sat by her with his legs crossed, neither saying anything. Mari liked having someone around, anyone around, and Shinji was that person. She knew that she had three sisters and deeply regretted, even at the age of eight, not getting to know any of them better, if at all. Her oldest sister had looked after Mari after her parents had died, if only for a brief time. Her mother had passed away in a car accident, while her father had been murdered several years after. It had been four years since she had seen her oldest sister, and her face was quickly fading in memory, slowly becoming a black silhouette with no features, only slight details that Mari was sure of. She knew her older sister had the same brunette hair as Mari herself, along with the same bright green eyes. Other than those details, Mari had forgotten everything, even the sound of her voice.

Mari's father had not been the most faithful husband, and as far as Mari knew, he had slept with more than one of the younger scientists under his command. The result had been two half sisters with different mothers. She had met one of them when she was four, only slightly younger than Mari herself, both of them born within the same six month interval. She didn't really remember much about her though, and even after intense thought could only come to the conclusion she was sure the girl had bright blue eyes.

Shinji was her brother too, if not genetically, at least emotionally. As much as she wanted to meet and spend time with her siblings, he was the one here, and thus the most important to her. She didn't really like poking at him the way she had to for attention, but it was better than nothing when he went off on his own. She slid towards him as she lay, wrapping her arms around the other child.

Shinji smiled lightly. He knew Mari didn't mean anything when she tormented him, other pining for affection. In all honesty once it was all said and done, he was strangely content with her.

"If you want to be a superhero, then I want to be one too." Mari said in a low voice. At that she rose and pulled the dark haired child with her. Nancy glanced up as the pair ran past the living room again, passively looking after the two. As the two children dug through their clothing together in search of acceptable superhero outfits, neither would have guessed that in no more than a few years that this childhood dream would be granted in more ways than one.

* * *

Mari hated when Shinji was like this. She sat by the bathroom door, her legs pulled to her chest, intently listening to the occupants as she sat. She flinched as she heard the sound of shattering glass, followed by Shinji screaming.

"H-how do I know what's real..." Shinji gasped between screams, Mari pulling her legs closer and burying her face in her knees. He would have nightmares from time to time. Afterwards he was never quite himself. Mari had hoped they would go away, but over the past few years, they only seemed to be increasing in frequency. Shinji himself had told her that he wasn't completely sure why he reacted the way he did, but ultimately he felt it was best if he just let it out. At fourteen years old though, it was quickly becoming more apparent how real his rage could be.

_He had told Mari about some of his dreams. Sometimes waking up on a desolate beach, no one in sight save a single girl. He had told Mari she looked a bit like herself. He had dove for her, trying to kill her, only to stop when her hand brushed against his face for a brief moment. She had the softest, most tender expression in her eyes and he could never go through with it. The feeling he felt from that single touch was maddening, and he had thrown himself off of her and cried. He had looked up with tears in his eyes, a vast blood red ocean before him, the smell so pungent and strong he had vomited on himself..._

_Other times he would awaken in an unfamiliar bed, the same girl yelling at him for some reason. He would scramble to get dressed, race by his parents and out the door with her. What he remembered from this dream so vividly were his parents, both him real mother and father quietly sitting in the kitchen preparing for their day, his mom's warm face as she waved goodbye, while his dad gave him a confident smirk. He remembered getting yanked along by this redhead girl, being dragged to school in a frenzy…._

_Shinji had dreamed of others as well. They came and went, but there roles were mostly the same. He had encountered a beautiful violet haired woman several times, she had been his middle school teacher or even guardian at times. He had seen a blue-headed, red eyed girl standing with his father under an orange sunset, her alabaster skin setting off her striking features in ways he couldn't describe. Once or twice he had mistaken her for his mother in some dreams. Kaji had come into his dreams as well, and he feared for the man's life, as every vivid piece of imagery related to this man involved death..._

_The story of his life was built through these dreams, and while inconsistent at some points, it roughly ran the same path. He would live in the city of Tokyo-3, where he would pilot giant creatures known as Evangelions. He would eventually come to live in close proximity of this dark haired woman and a redhead girl roughly his age. He would be a pawn in his father's scheme, and slowly lose his sanity as the world collapsed around him, everything eventually going comfortably numb. In one last blaze of glory the world would live its last breath and then there would be nothing but him. The blue haired girl would have given her life to him for some reason, and he would be cast onto an empty beach where he would try in vain to kill the last other human in the world..._

"Shinji." Nancy's voice started softly, " You have to be strong."

"You think I don't know that?!" Shinji's voice cracked between sobs.

"Please." Nancy insisted, "They aren't dreams, I know, they're memories and you have them for a reason…."

"W-whyy?" He asked, his voice nearly inaudible.

"It's a second chance." She nearly whispered into his ear, "It's a chance to fix everything wrong with the world and save everyone. You chose this, you're the one that chose to give us all another chance. You thought humanity was worth saving."

"BUT WHY ME?" Shinji asked, nearly screaming at her.

Nancy took him into her arms, " I can't answer that, only you can. You could have just willed this world into perfection in your past life, but you chose to fight on your own terms. You did this for a reason. Trust me Shinji, it will make sense one day. It'll all be better."

Nancy wasn't sure what more she could do to comfort him. He was literally aware of what the world would soon require from him, and that many people had expectations for him to meet that were higher than he had ever dared to imagine. She silently watched as he composed himself to the best of his ability, finally exiting the bathroom and wandering to bed, Mari soon rising from her position and following behind him slowly.

The next few days yielded minor improvements in Shinji's mood. Mari had started by making him dinner in bed the first evening. He had greatly appreciated the gesture, mustering all of his will to give her a thankful smile. Nancy hadn't required them to continue training while Shinji's psyche recovered, but he and Mari had woken up the next morning and continued their training anyways. Both Nancy and Mari watched him intently, noticing the slightly listless but determined expression upon his face as he pushed his body to its limits. Mari had sat out in the garden as Shinji continued through the night. She watched as he held himself upside down, only supporting his body with a single arm while the other was folded behind his back. After several hours he flipped seamlessly to his feet, assaulting nearby training dummies with all his might, until finally focusing all his strength into a single punch, annihilating a dummy instantly. Mari had stopped him when he had continued to focus his increasingly blind rage on a large rock in the garden.

"SHINJI! DON'T!" Mari cried as she caught his second attempt to strike at the rock, "Please Shinji, stop!", Even though she had a tight grip on one of his arms, Shinji still made every attempt to swing once more with his other fist. Blood splattered as he swung against the rock, Mari finally releasing his arm and diving towards him, enveloping him in an embrace.

"Stop you idiot!" Mari yelled at him, finally getting his attention. At that, he collapsed to the ground, Mari being pulled with him.

"I'm sorry..." Shinji whispered as his body went limp in her embrace.

"It's alright, just don't hurt yourself if you don't have to!" She whispered back.

For a moment silence reigned. Shinji didn't move, and Mari only tightened her hold on him. The two only glanced up as they noticed chunks of rock falling away from the large boulder Shinji had just struck.

"Shinji?" Mari asked, " Did you just punch through solid rock?"

"Yes?" He replied, the two rising to inspect the damage. He had left a crater in the boulder. Bits and pieces of the rock lay at their feet. He could only think to examine his fists. At first glance his knuckles were impossibly bloody, but upon further inspection he began to notice a distinct lack of pain. Mere minutes ago, yes, his knuckles had been bleeding intensely. Walking to a nearby pond he rinsed what blood remained off of his fists, carefully examining himself in the dull moonlight. He could see his own wounds slowly closing before his eyes. He blinked a few times, still not entirely sure he could see himself indeed healing.

Mari gasped as she saw his wounds closing. It wasn't remotely natural. "How?" She asked, glancing from his fists to his eyes.

"I-I don't know." Shinji replied, " I should have broken my fingers or wrists or something...Is it just me?"

"One way to find out." Mari replied, soon producing a small pocket knife in one hand while she held the other outright for Shinji to see. With little hesitation she sliced across her palm, fresh blood seeping out instantly. Both watched as the flow of blood accelerated for a minute, and then began to slow. She soon crouched, dipping her hand in the clear pond water, rubbing any remaining blood away. When she removed it, the cut was nearly sealed back, almost as if it had never happened.

"Are we...not normal?" Shinji asked, "...Both of us?"

"No you aren't." Nancy replied, startling the two.

"W-what do you mean?" Mari turned, facing her guardian.

"Both of you were given a gift when you were younger. It came as an official order." Nancy stood before them in the moonlight, as the two stared at her, clearly shocked, " You were both given an experimental cocktail of mutagens. However none of the effects are visible until puberty, and what enhancements you have gained will only continue to advance until adulthood."

"But who...why would anyone give us this?" Shinji asked, almost angry.

"I'm not for certain, but I do happen to know that the mutations will render you inhuman enough that Third Impact won't effect you. That's only one of many possible reasons that I imagine you were given this 'gift'."

"Get some sleep.", Nancy flatly ordered, turning around before either could ask another question, "We're going to pay our old friend, the doctor, a visit."

* * *

"Dr. Akki!" Nancy happily greeted the white haired man as she entered the old man's small clinic, Shinji and Mari just behind her.

"It's already been a year?" The small old man joked as he returned Nancy's hug. Shinji and Mari politely waved. They had been to Dr. Akki's clinic many times for 'checkups', as the doctor and Nancy called them. Normally they would have thought this nothing more than just some normal parenting or some mandated protocol set forth by Nancy's superiors, but it was obvious now that this old man was more than he appeared.

"My, my!" The old man smiled at the two teens, " You two have certainly sprung up! I remember when you two barely came to my waist!"

Both merely smiled back and talked casually. What followed next was routine. They would have some blood samples taken, a full physical, the doctor would converse with each of them individually and then talk to Nancy in private.

"They both exhibit mild sociopathic tendencies." The old man jokingly replied to Nancy.

"What do you think?" Nancy replied as she crossed her arms.

"Mari. It's just Mari. She's like that. She's a narcissist, and appears to be a bit schizophrenic, but it really is just her way of opening up."

"What about Shinji?" Nancy glanced to the Doctor and back at the wall, listening intently.

"Mari has really rubbed off on him since I first saw the two. He's much more relaxed and open. Look at the way they sit sometimes. They both unwind in their chairs and let their bodies spread out. He used to tighten up in his seat, as if he didn't want other approaching him. Mari has done worlds of good for the boy. He's no longer the wimp that he was a few years ago. It was if I was talking to Mari, he was bursting with confidence."

"You think that's a good thing?" Nancy asked.

"Maybe. Possibly. Most likely." The old man shrugged, " The nightmares he experiences will pass. He's not a pussy. Hell, I think any of us would be alarmed if we were having memories from past lives come back to us. He'll deal with it like he's dealt with you and everything else this world has thrown at him. He's ready for his father."

"And physically?" Nancy smiled, the old man's words comforting her. She had been worried about Shinji lately, but the old doctor was right. Shinji hadn't run away. Once he had composed himself, he had started to instead push himself as hard as he could.

"Both of them could snap a tiger's neck.", Dr. Akki laughed, " The serum worked wonders for both of them. Never in my life have I seen even one person its worked so well on, though aside from making the pair immune to Third Impact, I'm not to sure as to why they would give children destined to pilot such enhancements."

"My guess is that they fully believe he's the Shinji that will break us out of this loop." Nancy smiled back, " I think they just want him to go in there as prepared as possible."

* * *

Shinji and Mari were a bit of professional criminals in more than one way. Under Nancy's guidance their secret lives had flourished, and in a few short years, they were nothing short of legends. At times they stole for sport, at other times they stopped criminals dubbed too dangerous to be allowed to be free. The first years of their teenage lives had been an explosion of vigilante acts, and their talent for espionage and theft was becoming more and more apparent.

Aside from many technical improvements, the overall design that Shinji had settled on all those years ago hadn't changed. His original costume idea had been that of a benevolent gentleman, and the dark, form fitting suit he had chosen reflected that well. He had used some of his accrued wealth from previous endeavors to custom order his latest from Italy. He was conscious to make sure this one fit well, yet still allowed him ample room to maneuver. His vest was a dull purple, while he wore a scarf in lieu of a tie. Along with a pair of deceptively comfortable black dress shoes, he had to agree, that if he didn't choose to wear a mask, he would be a fairly attractive gentleman. Sadly, hiding his appearance was most important and he had chosen a plain white mask with dark circular eyes, along with a simple red smile. It was plain, fairly blank, and easy to recreate if he ever needed to make another. He had chosen to wear a cape as he found it was excellent in concealing his movements in combat, as well as making his slim form look menacing in moonlight. Lastly came the light blue wig he had chosen after much debate. He wasn't one for anything too flashy, but he had settled on it as his search hadn't found too many wigs he felt that his appearance complemented.

Mari dressed in a similar fashion, clad in almost all black. Her v-neck top showed just a bit of her chest, while a pink scarf was wrapped around her neck. Her black coat was buttoned around her midsection, the long tail reaching just above her ankles. She had settled on a blonde wig, along with a pair of deep orange sunglasses to conceal her eyes.

Neither had chosen a particular name, alas their brand of justice and mischief tended to sell itself. To many they merely called him 'V', and her 'Lady V'. Shinji knew of a British movie that people were referencing, and laughed off the name with a shrug, guessing people could call them whatever they liked. In Japan however, he could only sigh, realizing that he appeared identical to a character in an anime he had watched as a child. 'The Phantom Renegade' was a joking name at first, but it had quickly stuck, and as the news articles mounted, each telling of his achievements, the name was starting to become mainstream. Mari had been lucky to merely be dubbed as the "Lady Phantom", to which she grinned at, absolutely enthralled with the idea of being a real vigilante with a signature appearance and style.

Their physical and mental abilities were known well around the world, however their 'super' powers had yet to be revealed, as neither had to put much effort or ability into any of their 'missions' thus far. Tonight was different however. Instead of working for themselves, they had been contracted. The orders had come through Kaji, and he in turn had contacted Nancy. She had frowned at first, but she reluctantly agreed, knowing that in all the years she had cared for the two, they had been sneaking off and performing their antics whether or not she actually approved. When she had brought the mission to her two children, both had agreed instantly, Shinji even wearing the same cocky smirk that Mari was so famous for.

"So this is Tokyo-3...", Shinji scoffed as he looked down from the back of the transport jet. He felt a certain animosity to the city below, as it currently housed his father. He desperately hoped that through any form of sheer luck he wouldn't run into his father on this mission. He wasn't sure he would be able to control himself, and feared deeply for what he might do. It wasn't Shinji himself that would strike out at his father, it was the Phantom. When he dawned the mask, his persona took over. Phantom Shinji was even more bold, reckless, haughty and overpowering. He always felt like a different person with the mask on, and he wasn't always sure of what he had done when he took the mask off. Mari didn't fair any better. She went from reckless and haughty to an all out adrenaline packed nightmare. She was fast paced, over the top, and almost more demonic than Shinji could be.

"What forces you two do encounter is all there will be." Kaji's voice cracked over their ear mounted communication devices, " We've given all other forces false orders to stand down inside the city, and I have jammed all communication between NERV and all other organizations for the next thirty minutes. Your drop zone is approaching, get ready."

"...Ready?" He asked Mari from behind his mask.

"Ready!" She replied, both ready to dive out of the airship and towards the ground below.

"SHOWTIME!" Shinji yelled in his boldest voice, letting himself fall forward and get sucked out of the plane as Mari jumped forward.

He always loved this part, whether it be jumping off a building or out of a plane, the momentary sense of weightlessness that falling allowed him was incredibly exhilarating. It made his heart flutter with excitement, and was the perfect way to start the rush that he was about to experience. Mentally counting down, he deployed his parachute exactly on mark, gently guiding himself in the brisk night wind towards the target building. A pair of VTOLs would be landing soon, the NERV transport crafts carrying his targets. He and Mari were to land just as the target packages were being transferred into the building. At least a dozen guards would be present, and it would be there mission to slip in, and leave before NERV could even realize what was going on.

As they approached, the VTOLs neared, right on time. There was a team of guards already visible on the rooftop, with no doubt more in each transport. He and Mari would attack from the sky, dropping in upon them, letting the darkness be their greatest ally. He watched below as the aircraft's guards disembarked, one from each carrying a black briefcase, no doubt the packages the pair had been sent for.

He could feel his heart beating as he prepared to undo his parachute harness. He waited for the perfect moment, descending upon the armed guards in a fell swoop.

"BWAHAHAHAHA…." Phantom Shinji laughed maniacally from above.

There was confusion for a few moments as guards dropped like flies, the remaining men looking around in confusion, unsure of which direction their assailants were coming from, the only clue being the knives that had hit their mark. The Phantom descended from the sky, instantly incapacitating the guards he landed on, while the Lady Phantom dropped from above just a moment later, sending two guards flying in one fluent kick. What had been a combined detail of no more than eighteen was now cut down to six. Bullets flew as the remaining men unloaded upon their targets, the black figures they sought to bring down hopelessly faster than they could even aim. In a few more moments it was over as each man slowly fell to the floor, no one entirely sure whether or not they had been struck once or multiple times.

"I'll take these." The Phantom chuckled as he opened one of the briefcases. Inside there were two canisters, Shinji taking each and stowing them in his jacket, while Mari did the same with the contents of the other suitcase, their thick leather gloves hiding any fingerprints that anyone would hope to find.

"What do you think these are?" Phantom Mari asked as she inspected the contents.

"Better not to ask." He replied. That moment sirens and alarms could be heard in the distance. Guards began exploding through the doors leading to the rooftop, both Phantoms sprinting to the nearest edge and diving off the top of the skyscraper. This would be the difficult part. Getting into the city was easy, however extraction was trickier. They were to travel to a distant building that had been determined before hand, and wait for the extraction team to rendezvous with them.

* * *

"No response from JSSDF forces!" Misato Katsuragi spun around.

"What?" Gendo Ikari spat back as he rose from his commanding position.

"We can't make contact with them. All of their forces have retreated to encircle the city." Misato sighed, " It's as if they're proceeding with our protocols to defend against an all out assault from an Angel."

Gendo Ikari merely listened, trying to compose himself. He was angry, absolutely livid, but did his best to hide it. It was rare when situations such as this caused him to emote, but more was on the line in this single moment than any of his subordinates realized.

"Section 2 and all remaining defense forces are doing there best, however they can't keep up with the targets." Misato continued. The dark haired woman stood expectantly, arms crossed, waiting for her commander's response, "They're dropping like flies out there."

"Any information concerning where the targets are heading?" Commander Ikari asked thoughtfully as he placed his hands behind his back.

"No." Misato sighed, "They just continue to evade our forces."

"And how many of our personnel and aircraft have fallen to them?"

"Approximately sixty of our own, and at least 12 aircraft."

Gendo clenched his fist at this. Failure was not an option now. Never before had any of his dealings been intercepted. They obviously knew far more than Gendo had ever expected, and had chosen this specific exchange for a multitude of reasons. The dark haired man was in too deep to stop now, and he knew that without the assistance of the Japanese military, NERV wasn't equipped to deal with such a strike. Somehow, their assailants had given the JSSDF false orders, and now NERV had lost all communication with them as well. His options were dwindling quickly, and it could be mere minutes before his packages were lost forever.

"Is Unit Zero still in staging?" Gendo finally asked.

"Y-yes sir?" Misato sputtered out, shocked that her superior would be asking that now of all times, " Rei is is still in the entry plug. The post tests concluded just before we were assaulted."

"Good." Gendo smiled, "Prepare Unit Zero for launch immediately."

"You can't be serious." Misato replied in disbelief.

"Desperate times call for desperate measures."

* * *

"SHINJI! MOVE!" Kaji's voice desperately cracked over the communication link.

"What? Why?" Shinji asked as he flew through the air, about to land on another rooftop.

No sooner did he ask, his answer coming to him. He contorted his body as best he could, narrowly dodging a giant hand as it reached for him. The sheer size of the godlike arm reaching for him caused the wind to whip unpredictably, throwing him around like a rag doll as he did his best to land on his feet, rolling onto the roof of a nearby building. He looked up only a moment to see a giant cyclops form towering above him.

"It's Eva Unit Zero!" Kaji's voice cracked once more, "Your father ordered the launch!"

Shinji looked up, acknowledging the giant armored behemoth that stood before him, the creature looking down at him.

"I'll deal with it." Shinji replied to Kaji. Mari was nowhere to be seen. They had momentarily split up minutes ago. It was just him against a behemoth. The creature reared back to strike once more, Shinji noticing that while it's aim was true, the creature itself was not entirely in control of it's own body. As he jumped, narrowly dodging another reaching hand, he looked for a weakness, the cyclopean eye seeming to be his only option for attack.

"BWAHAHAHAA!" Phantom Shinji laughed maniacally, " I know that you can hear me Commander Ikari…"

Phantom Shinji revealed a grappling gun, shooting to a radio tower on a nearby building, swinging away from the Eva's next assault only to whip around the radio tower and come to stand where he originally started.

"….Tell me Commander, do you wear boxers or briefs?" Phantom Shinji continued. Once more Unit Zero came at him, the building below finally crumbling as the Phantom produced a second grappling gun, the first still in hand. He shot again, only in the opposite direction this time, the tip finding its mark in a nearby tree. He jumped up, catching the back of the Eva's hand as the creature's reach extended.

"In the end, I guess it doesn't matter Commander, for you see, all that matters in the end is the elasticity that a waste band provides… It can be the difference between slight amusement and utter embarrassment when you're caught with your pants down..."

Shinji's plan had come together. Both of his grapple lines held, and he had carefully planted his feet on back of Unit Zero's outreached hand as it had tried to grab for him, both lines he held onto had stretched, finally pulling taught. At that moment he had jumped up and forward over the Eva's hand,the force from both lines propelling his body explosively towards the Evangelion's large single eye. In sheer seconds he produced a sword from under his cape, his momentum propelling him and the sword through the Eva's eye, the lens shattering as he disappeared inside. Blood exploded from the creature as it threw its head back in pain.

Shinji soon reappeared, diving out of the massive wound, covered in deep red blood.

"Shinji!" Kaji's voice came over the comm link, " It's beginning to berserk! Finish it!"

"Gotcha!" Shinji quickly produced a handheld explosive device from his coat, " I got just the thing." Shinji tapped a few buttons on the device, calmly standing as the creature before him began to thrash about, destroying nearby buildings. As the creature swung wildly, he managed to suddenly jump onto it's outreached arm, catching a grip on its heavy armor. Quickly he ran up its arm, dodging several pieces of debris and once using a knife to maintain his grip as the creature rampaged wildly. Jumping from the shoulder, he landed on it's skyward face, fresh blood pouring out of it's completely destroyed eye. With all of his might he reared his arm back, throwing the explosives with all of his force. Several moments later he managed to jump for safety, narrowly landing on a nearby rooftop. Giving one last mighty cry, the creature's head exploded, blood splattering on nearby buildings, the large body crumpling to its knees. The body slumped over onto the nearby streets, blood beginning to pool around it.

"W-what?" Misato's jaw dropped as she watched the battle, " She couldn't activate her AT field in time..."

**Prologue Pt 02: END**

* * *

**SIDESTORY 01:**

**Here's something from the scrap pile as I've been working on future chapters. Let me know if you like it or not! A tad of Shinji x Asuka for you!**

Several Months Later...

Mari wasn't in the mood to pester anyone else on the ship, _Over The Rainbow_. Returning to her cabin, she found Shinji asleep in one bed and Asuka asleep in the other. She hadn't been able to stand the pair's bickering and had opted to have a cigarette or two with Kaji instead. Since both of them were asleep Mari changed out of her school uniform and into her night clothes in the open cabin. Asuka had been obstinate of Shinji's presence even after Kaji had insisted they 'get to know each other'. Shinji had cursed at her for being so obnoxious and the two had gone off from there. Mari, in her infinite wisdom, wasn't sure if they absolutely hated each other or were absolutely in love as their bickering was unlike any force she had yet to experience. Asuka went out of her way to torment him and he absolutely let his mouth speak his mind in front of her. One thing she was certain of was that a cloud of sexual tension the size of Japan was developing between the two.

Mari had quickly realized that she did not have a bed. Somehow in the shuffle of the day, she had just assumed she was going to continue bunking in the same room with Asuka, however apparently they had delegated Shinji as her new roommate. No one had given it a second thought, and Mari found herself with a bit of a predicament. Asuka had sprawled out across her own bed just the way Mari liked, and there was no way that Mari was sharing a bed with either one, instead she wanted one of their beds for herself.

"Shinji, move over, I'm sleeping with you." She whispered into the young man's ear.

Shinji merely grunted as he made room in the small bed for a second person. Mari smiled, hopping back over to Asuka as she lay sprawled in the opposite bed.

"Asuka, I'm going to sleep with you, alright?" Mari whispered into Asuka's ear.

"O-Okay." Asuka replied groggily, as she scooted over a bit. Mari knew that Asuka could be a heavy sleeper. Carefully Mari lifted her, transplanting the redhead from one bed to the other. She placed the girl into Shinji's bed, soon admiring her work. Asuka pressed into Shinji as she got comfortable. Mari couldn't help but smile.

"Hold me, baka." Mari whispered to the two. Both acknowledged Mari's command, blissfully unaware that the other was not Mari, their arms wrapping around each other, the two pulling their bodies tight together.

Mari produced her smartphone, capturing a few pictures of the two cuddled together before returning to her own freshly claimed bed. She would post these pictures to various social pages in the morning. For a few minutes she watched as Asuka and Shinji rolled around, adjusting themselves. Asuka soon found herself sleeping contently as Shinji's arms wrapped around her body, her back pressed firmly into his chest and stomach.

"...Warm...", A single word escaped Asuka's lips.

Mari flipped around in bed at this, her legs kicking wildly. She was absolutely dazzled. She loved the idea of her sibling and her best friend together. They looked cute enough. She deeply hoped it would happen.

...

Morning came soon enough. Mari scampered out of the cabin as quick as possible. Shinji and Asuka had woken each other up, immediately thrown their arms off each other, and exploded angrily at Mari. The brunette had barely grabbed her glasses and cellphone as the dark haired boy and redhead girl tossed shoes and other random items at her. She laughed gingerly, their guardians, Misato and Kaji happening to be walking down the hall.

"What's going on Mari?" Misato asked as the door to their cabin slammed shut behind Mari, both Japanese and German curses being yelled in tandem from behind the door.

"Shinji and Asuka are being mean." Mari said in her cutest voice, "I caught them sleeping together and they chased me out of their cabin." At this Mari showed both Kaji and Misato the images on her phone, the two guardians smiling warmly at pictures of the two cuddled close.

"I think I really misjudged Shinji." Misato smirked, "Beneath that kind and innocent exterior he's really a smooth operator."

**SIDESTORY 01 END.**

* * *

**Alrighty guys, we're nearly done with the prologue chapters! After this there's just one more prologue, and then we will arrive at our first real chapter,01: OVER THE RAINBOW! I promise I'll do my best to make the wait worth it! As always, let me know how I did!**


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